Source code for deeprank.targets.capri_class

import warnings

import numpy as np
from pdb2sql import StructureSimilarity

from deeprank.targets import rmsd_fnat


def __compute_target__(decoy, targrp):
    """Calculate CAPRI class.

        CAPRI class name and ID:
            - 'high': 0
            - 'medium': 1
            - 'accepetable': 2
            - 'incorrect': 3

    Args:
        decoy(bytes): pdb data of the decoy
        targrp(hdf5 file handle): HDF5 'targets' group
    """
    categories = {'high': 0,
                  'medium': 1,
                  'accepetable': 2,
                  'incorrect': 3}

    tarname = 'CAPRI_CLASS'
    if tarname in targrp.keys():
        del targrp[tarname]
        warnings.warn(f"Removed old {tarname} from {targrp.parent.name}")

    tarelems = ['FNAT', 'LRMSD', 'IRMSD']
    vals = {}
    for tarelem in tarelems:
        # if target element exist, then use its value; otherwise calculate it
        if tarelem not in targrp:
            _ = rmsd_fnat.__compute_target__(decoy, targrp, tarelem)
        # empty dataset
        elif targrp[tarelem][()].shape is None:
            _ = rmsd_fnat.__compute_target__(decoy, targrp, tarelem)

        # get the value
        vals[tarelem] = targrp[tarelem][()]

    label = StructureSimilarity.compute_CapriClass(
                vals['FNAT'], vals['LRMSD'], vals['IRMSD'])
    targrp.create_dataset(tarname, data=np.array(categories[label]))